The FBI has found that a business associate of former Trump campaign chairman Paul Manafort had ongoing ties to Russian intelligence, including during the 2016 presidential campaign when Manafort and his deputy, Rick Gates, were in touch with the associate, according to new court filings.

The documents, filed late Tuesday by prosecutors for special counsel Robert S. Mueller III, also allege that Gates has said he knew the associate was a former officer with the Russian military intelligence service.

The allegations underscore Mueller’s interest in Manafort and Gates, who continued to interact with business associates in Ukraine even as they helped lead Donald Trump’s presidential campaign.

Manafort, 68, has pleaded not guilty to conspiracy, money laundering, and tax and bank fraud charges related to his lobbying work for a pro-Russian political party in Ukraine and former Ukrainian president Viktor Yanukovych.

Gates, 45, who was deputy campaign manager for Trump and had earlier worked with Manafort in Ukraine, pleaded guilty last month to conspiracy and lying to the FBI in a cooperation deal with Mueller’s probe.

Prosecutors made the allegation without naming the Manafort associate but described his role with Manafort in detail. The description matches Konstantin Kilimnik, the Russian manager of Manafort’s lobbying office in the Ukrainian capital, Kiev.

Kilimnik did not respond to a request for comment. Nor did a White House spokesman or an attorney for Gates.

Kilimnik has previously denied intelligence ties, telling The Washington Post in a statement in June that he has “no relation to the Russian or any other intelligence service.”

A spokesman for Manafort, who is under a court gag order, declined to comment.

Manafort has acknowledged staying in frequent contact with Kilimnik during the time he worked for Trump’s campaign. He has said he met with Kilimnik in person in May 2016 and again in New York City in August 2016, about two weeks before Manafort resigned as Trump’s campaign chairman.

A Manafort spokesman expressed confidence in June that investigators would ultimately conclude that Manafort’s interactions with Kilimnik were “perfectly permissible and not in furtherance of some conspiracy.”

The information about the FBI’s assessment of the Manafort associate came in a court filing related to the upcoming sentencing of London attorney Alex van der Zwaan, whose firm worked with Manafort when he served as a political consultant in Ukraine.

Van der Zwaan, 33, the son-in-law of a prominent Russian Ukrainian banker, pleaded guilty last month to lying about his September 2016 contacts with Gates and the Manafort associate, identified in court documents only as “Person A.”

Prosecutors explained that van der Zwaan had lied and withheld documents about information that was “pertinent” to their investigation — that Gates had been in direct contact during the presidential campaign with a person who “has ties to a Russian intelligence service and had such ties in 2016.”

They said that when van der Zwaan was interviewed by the FBI in November, he told investigators that Gates had informed him that Person A was a former officer of the Russian military intelligence service, known as the GRU.

Kilimnik ran Manafort’s office in Kiev during the 10 years he did consulting work there, The Post reported in 2017.

During his August 2016 meeting with Kilimnik, Manafort has said he and his longtime Kiev office manager discussed, among other topics, the ongoing campaign, including the hacking of Democratic National Committee emails. Stolen DNC emails had been released by WikiLeaks the previous month, and the hack was widely suspected to be the work of Russia.

During Kilimnik’s time working for Manafort in Kiev, he had served as a liaison for Manafort to the Russian aluminum magnate Oleg Deripaska, with whom Manafort had done business. Emails previously described to The Post show that Manafort asked Kilimnik during the campaign to offer Deripaska “private briefings” about Trump’s effort. A Deripaska spokeswoman has said the billionaire, a close ally of Russian President Vladimir Putin, was not offered and did not receive such briefings.

Kilimnik previously told The Post that he had served for a time in the early 1990s in the Russian army, but he denied any links to intelligence work.

Manafort has also denied knowingly communicating with Russian intelligence during the campaign. He told the New York Times last year, however, “It’s not like these people wear badges that say, ‘I’m a Russian intelligence officer.’ ”